COURSE UNIT TITLE

: COMPUTATIONAL BIOPHYSICS

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
MBG 6135 COMPUTATIONAL BIOPHYSICS ELECTIVE 3 0 0 12

Offered By

Molecular Biology and Genetics

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

ASSISTANT PROFESSOR EZGI KARACA EREK

Offered to

Molecular Biology and Genetics
Molecular Biology and Genetics

Course Objective

To have a comprehensive understanding of how biomolecular behavior can be dissected through physics.

Learning Outcomes of the Course Unit

1   1. Learning basic physics and mathematics tools required to understand biological processes
2   2. Learning how to combine physics and mathematics to dissect complex biological phenomena
3   3. Learning biophysical experimental techniques
4   4. Learning how to code and run in silico biophysical simulations
5   5. Learning how to combine experimental and in silico techniques in order to solve complex biological problems

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Structural Methods - NMR
2 Structural Methods - X-ray
3 Structural Methods - EM
4 Molecular and Mechanical Forces
5 Macromolecular Conformations
6 Spectroscopic Methods
7 Molecular Recognition and ligand binding
8 Diffusion and Brownian Motion
9 Binding affinity experiments
10 Physics-based molecular dynamics simulations
11 Biological membranes
12 Electrical properties of molecules and ion channels
13 Dynamic scattering and SAXS
14 Hydrodynamics-based experimental techniques
15 Microscopy-based techniques
16 Final exam

Recomended or Required Reading

P. Nelson, "Biological Physics" WH Freeman, 2004
K.A. Dill et al, "Molecular Driving Forces" Garland Science, 2003
M. B. Jackson: "Molecular and Cellular Biophysics" Cambridge U. Press, 2006
A.E. Leach, Molecular Modelling: Principles and Applications, 2nd edition
C. Brandon & J. Tooze, Introduction to Protein Structure, 2nd edition

Planned Learning Activities and Teaching Methods

Theoretical PowerPoint lectures with literature review/discussion, applied computer practicals.

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA
1 ASG ASSIGNMENT
2 MTE MIDTERM EXAM
3 FIN FINAL EXAM
4 FCG FINAL COURSE GRADE ASG * 0.30 + MTE * 0.30 + FIN * 0.40
5 RST RESIT
6 FCGR FINAL COURSE GRADE (RESIT) ASG * 0.30 + MTE * 0.30 + RST * 0.40


Further Notes About Assessment Methods

None

Assessment Criteria

One minute paper should be delivered by the end of each lecture to the instructor. This paper should contain a couple of sentences summarizing what was taught during the lecture.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

ezg.karaca@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 15 3 45
Preparations before/after weekly lectures 14 8 112
Preparation for final exam 1 30 30
Preparing assignments 2 20 40
Project Preparation 1 45 45
Preparing presentations 2 15 30
Final 1 5 5
TOTAL WORKLOAD (hours) 307

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8
LO.1545
LO.254445
LO.354444
LO.44444
LO.54444

CONTACT INFORMATION
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Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

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